[gmx-users] how to add angle_restraints and dihedral_restraints for atoms belonging to two different molecules

[Mark Abraham]

On Sat, May 18, 2013 at 10:20 AM, jnsong <jnsong at itcs.ecnu.edu.cn> wrote:

> Dear all,
>
> Recently, I want to add angle_restraints and dihedral_restraints for atoms
> in two separate molecules, that is, inter-molecular restraints, not
> intra-molecular restraints.
>
> I add the following into my .top file:
> [ angle_restraints ]
> ; i   j    k    l    type   theta0     fc     multiplicity
>  20  22   47   50    1      0.0       1500         1
>
> [ dihedral_restraints ]
> ;   i    j     k    l    type label phi dphi kfac power
>    25   28    51   52     1      1 180     0     1      2
>
> But it give errors:
> "Fatal error:
> [ file ang_res.itp, line 5 ]:
> Atom index (47) in angle_restraints out of bounds (1-24).
> This probably means that you have inserted topology section
> "angle_restraints"
> in a part belonging to a different molecule than you intended to."
>
> Atom 20/22 belongs to one molecule, and Atom 47/50 belongs to another
> molecule. The same situation is for atom 25/28 and atom 51/52.
>
> I guess this error comes from the fact that I have two separate molecules
> in my simulation system, thus topol_Protein.itp and topol_Protein2.itp are
> produced when using pdb2gmx. Atom 47 in .gro file has atom number 17 in
> topol_Protein2.itp. Thus it gives the error that Atom index (47) in
> angle_restraints out of bounds!
>
> Additionally, [ angle_restraints] and [dihedral_restraints] seems for the
> intra-molecular interaction definitions.
>
> Would you please tell me how to add angle and dihedral restraints for the
> atoms that belong to two different molecules?
>

You need both molecules in the same [moleculetype], since the restraint
directives require this.

pdb2gmx -h will help here.

Mark